Bali-Phy REST

Bali-Phy3 XSEDE REST interface: BALI_PHY3_XSEDE

This interface is used from the REST API to configure BaliPhy3 runs. One can use a configuration file to set run params, or set specific switches to configure the run.

The setup is to run the analysis on a single core. You can achieve parallelization by creating multiple runs.

The Tool ID for this interface is tool=BALI_PHY3_XSEDE

Supported parameters:

Input files

input.input_file_ - Primary Input File (First gene to analyze)
input.input_file2_ - Specify a second input file (Secon gene to analyze)
input.input_file3_ - Specify a third input file (Third gene to analyze)
input.input_file4_ - Specify a fourth input file ((Fourth gene to analyze)
input.input_file5_ - Specify a fifth input file (Fifth gene to analyze)
input.input_file6_ - Specify a sixth input file (Sixth gene to analyze)
input.config_file_ - Specify a config file
input.tree_file_ - Specify a starting tree

Visible Parameters

vparam.runtime_ - (Float) maximum number of hours to run (default=0.5)
vparam.test_only_ - (Switch) Analyze the initial values and exit.
vparam.directory_name_ - (String) Name for the analysis directory to create.
vparam.num_iterations_ - (Integer) Number of iterations to run (-i); default = 200000.
vparam.datatype_ - (Excl) Choose the data type for Gene 1 (--alphabet) Values: DNA, RNA, Amino-Acids, Codons, Triplet.
vparam.substitution_model_ - (Excl) Choose the Substitution Model for Gene 1 (-S). Values: f81; hky85; tn93; gtr; HKYx3; TNx3; GTRx3; jtt; wag; lg08; gy94; gtr_sym+gy94
vparam.custom_model_ - (String) Enter a custom substitution model for Gene 1
vparam.gammarates41_ - (Excl) Use Gamma[4] for Gene 1 Values: +Rates.Gamma[4] or no entry.
vparam.invariable1_ - (Excl) Allow invariant sites for Gene 1 Value: +inv or no entry .
vparam.model_type_1 - (Excl) Estimate the insertion-deletion model for Gene 1 (-I) Values: RS07, none.
vparam.datatype_2_ - (Excl) Choose the data type for Gene 2 (--alphabet) Values: DNA, RNA, Amino-Acids, Codons, Triplets.
vparam.substitution_model2_ - (Excl) Choose the Substitution Model for Gene 2 (-S). Values: f81; hky85; tn93; gtr; HKYx3; TNx3; GTRx3; jtt; wag; lg08; gy94; gtr_sym+gy94
vparam.custom_model2_ - (String) Enter a custom substitution model for Gene 2
vparam.gammarates42_ - (Excl) Use Gamma[4] for Gene 2 values: +Rates.Gamma[4] or no entry.
vparam.invariable2_ - (Excl) Allow invariant sites for Gene 2 Value +inv or no entry.
vparam.model_type_2_- (Excl) Estimate the insertion-deletion model for Gene 2 (-I) Values: RS07, no entry.
vparam.datatype_3_ - (Excl) Choose the data type for Gene 3 (--alphabet) Values: DNA, RNA, Amino-Acids, Codons, Triplets.
vparam.substitution_model3_ - (Excl) Choose the Substitution Model for Gene 3 (-S). Values: f81; hky85; tn93; gtr; HKYx3; TNx3; GTRx3; jtt; wag; lg08; gy94; gtr_sym+gy94
vparam.custom_model3_ - (String) Enter a custom substitution model for Gene 3
vparam.gammarates43_ - (Excl) Use Gamma[4] for Gene 3 values: +Rates.Gamma[4] or no entry.
vparam.invariable3_ - (Excl) Allow invariant sites for Gene  Value +inv or no entry.
vparam.model_type_3_- (Excl) Estimate the insertion-deletion model for Gene 3 (-I) Values: RS07, no entry.
vparam.datatype_4_ - (Excl) Choose the data type for Gene 3 (--alphabet) Values: DNA, RNA, Amino-Acids, Codons, Triplets.
vparam.substitution_model4_ - (Excl) Choose the Substitution Model for Gene 4 (-S). Values: f81; hky85; tn93; gtr; HKYx3; TNx3; jtt; GTRx3; wag; lg08; gy94; gtr_sym+gy94
vparam.custom_model4_ - (String) Enter a custom substitution model for Gene 4
vparam.gammarates44_ - (Excl) Use Gamma[4] for Gene 4 values: +Rates.Gamma[4] or no entry.
vparam.invariable4_ - (Excl) Allow invariant sites for Gene 4 Value +inv or no entry.
vparam.model_type_4_- (Excl) Estimate the insertion-deletion model for Gene 4 (-I) Values: RS07, or no entry.
vparam.datatype_5_ - (Excl) Choose the data type for Gene 5 (--alphabet) Values: DNA, RNA, Amino-Acids, Codons, Triplets.
vparam.substitution_model5_ - (Excl) Choose the Substitution Model for Gene 5 (-S). Values: f81; hky85; tn93; gtr; HKYx3; TNx3; jtt; GTRx3; wag; lg08; gy94; gtr_sym+gy94
vparam.custom_model5_ - (String) Enter a custom substitution model for Gene 5
vparam.gammarates45_ - (Excl) Use Gamma[4] for Gene 5 values: +Rates.Gamma[4] or no entry.
vparam.invariable5_ - (Excl) Allow invariant sites for Gene 5 Value +inv r no entry.
vparam.model_type_5_- (Excl) Estimate the insertion-deletion model for Gene 5 (-I) Values: RS07, no entry.
vparam.datatype_6_ - (Excl) Choose the data type for Gene 6 (--alphabet) Values: DNA, RNA, Amino-Acids, Codons, Triplets.
vparam.substitution_model6_ - (Excl) Choose the Substitution Model for Gene 6 (-S). Values: f81; hky85; tn93; gtr; HKYx3; TNx3; jtt; GTRx3; wag; lg08; gy94; gtr_sym+gy94
vparam.custom_model6_ - (String) Enter a custom substitution model for Gene 6
vparam.gammarates46_ - (Excl) Use Gamma[4] for Gene 6 values: +GammaRates[4] or no entry.
vparam.invariable6_ - (Excl) Allow invariant sites for Gene 6  Value +inv or no entry.
vparam.model_type_6_- (Excl) Estimate the insertion-deletion model for Gene 6 (-I) Values: RS07 or no entry.
vparam.subsample_factor_ - (Integer) Factor by which to subsample (-x)  Default=1
vparam.random_seed_ - (Integer) Random seed (-s)  
vparam.linkfile1_ - (Excl) Values 1,2,3,4,5,6 Select the first gene to link; choose the lowest value first; Choose at least two.
vparam.linkfile2_ - (Excl) Values 1,2,3,4,5,6 Select the first gene to link; choose the lowest value first; Choose at least two.
vparam.linkfile3_ - (Excl) Values 1,2,3,4,5,6 Select the first gene to link; choose the lowest value first.
vparam.linkfile4_ - (Excl) Values 1,2,3,4,5,6 Select the first gene to link; choose the lowest value first.
vparam.linkfile5_ - (Excl) Values 1,2,3,4,5,6 Select the first gene to link; choose the lowest value first.
vparam.linkfile6_ - (Excl) Values 1,2,3,4,5,6 Select the first gene to link; choose the lowest value first.
vparam.linkfile21_ - (Excl) Values 1,2,3,4,5,6 Select a Second group of genes to link; choose the lowest value first; Choose at least two.
vparam.linkfile22_ - (Excl) Values 1,2,3,4,5,6 Select a Second group of genes to link; choose the lowest value first; Choose at least two.
vparam.linkfile23_ - (Excl) Values 1,2,3,4,5,6 Select a Second group of genes to link; choose the lowest value first.
vparam.linkfile24_ - (Excl) Values 1,2,3,4,5,6 Select a Second group of genes to link; choose the lowest value first.